seqtk ☆

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Description:
Toolkit for processing sequences in FASTA/Q formats

Type: Formula | Tracked Since: Dec 28, 2025

Links: Homepage | formulae.brew.sh

Category: Other

Tags: bioinformatics genomics sequence-analysis cli fasta fastq

Install: brew install seqtk

About:
Seqtk is a powerful command-line tool for processing nucleotide and protein sequences in FASTA and FASTQ formats. It provides a comprehensive suite of utilities for common tasks like subsetting, filtering, and converting sequence data. Its efficiency and lightweight design make it a staple in bioinformatics workflows for handling large genomic datasets.

Key Features:

Efficiently extract and subset sequences from large files
Filter sequences based on quality scores, length, and headers
Convert between FASTA and FASTQ formats
Perform sequence manipulation like reverse complementing and masking

Use Cases:

Preparing read data for genome assembly by filtering out low-quality sequences
Subsetting a large reference genome to a specific set of regions for targeted analysis
Converting FASTQ files to FASTA format for compatibility with alignment tools

Alternatives:

bioawk – A more general-purpose awk for bioinformatics formats, but seqtk is more specialized for common sequence manipulation tasks.
samtools faidx – Excellent for indexed reference genomes, but seqtk offers more versatile filtering and format conversion for read data.

Version History

Detected	Version	Rev	Change	Commit
Sep 16, 2025 10:17am		0	VERSION_BUMP	dc6b51be
Sep 14, 2024 5:27pm		0	VERSION_BUMP	e9eb1abe